Starting phenix.real_space_refine on Fri May 9 14:51:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bhb_44539/05_2025/9bhb_44539.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bhb_44539/05_2025/9bhb_44539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bhb_44539/05_2025/9bhb_44539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bhb_44539/05_2025/9bhb_44539.map" model { file = "/net/cci-nas-00/data/ceres_data/9bhb_44539/05_2025/9bhb_44539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bhb_44539/05_2025/9bhb_44539.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 1681 2.51 5 N 441 2.21 5 O 494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2626 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 931 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "K" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 841 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "A" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 854 Classifications: {'peptide': 98} Link IDs: {'TRANS': 97} Chain breaks: 3 Time building chain proxies: 2.88, per 1000 atoms: 1.10 Number of scatterers: 2626 At special positions: 0 Unit cell: (55.1, 64.525, 91.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 494 8.00 N 441 7.00 C 1681 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 308.5 milliseconds 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 612 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 7 sheets defined 29.9% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.516A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.781A pdb=" N ASP H 86 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR H 87 " --> pdb=" O ASP H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.964A pdb=" N PHE K 83 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 600 Processing helix chain 'A' and resid 622 through 640 removed outlier: 3.771A pdb=" N LYS A 638 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 639 " --> pdb=" O GLU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 672 removed outlier: 4.278A pdb=" N GLU A 671 " --> pdb=" O HIS A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 693 removed outlier: 3.777A pdb=" N TRP A 678 " --> pdb=" O LYS A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 717 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.560A pdb=" N ALA H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER H 110 " --> pdb=" O ALA H 10 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.560A pdb=" N ALA H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER H 110 " --> pdb=" O ALA H 10 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 17 through 20 removed outlier: 3.540A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.869A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE K 48 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 19 through 20 113 hydrogen bonds defined for protein. 297 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.68 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 812 1.34 - 1.46: 562 1.46 - 1.57: 1300 1.57 - 1.69: 0 1.69 - 1.81: 14 Bond restraints: 2688 Sorted by residual: bond pdb=" N SER K 7 " pdb=" CA SER K 7 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 9.51e+00 bond pdb=" N VAL K 3 " pdb=" CA VAL K 3 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.27e-02 6.20e+03 8.23e+00 bond pdb=" N GLU K 17 " pdb=" CA GLU K 17 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.16e-02 7.43e+03 7.79e+00 bond pdb=" N LEU K 13 " pdb=" CA LEU K 13 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.27e-02 6.20e+03 6.85e+00 bond pdb=" N ASP K 18 " pdb=" CA ASP K 18 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.33e-02 5.65e+03 6.59e+00 ... (remaining 2683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 3365 1.42 - 2.84: 217 2.84 - 4.25: 35 4.25 - 5.67: 9 5.67 - 7.09: 4 Bond angle restraints: 3630 Sorted by residual: angle pdb=" N ILE H 53 " pdb=" CA ILE H 53 " pdb=" C ILE H 53 " ideal model delta sigma weight residual 109.34 102.25 7.09 2.08e+00 2.31e-01 1.16e+01 angle pdb=" C ASP K 50 " pdb=" N ALA K 51 " pdb=" CA ALA K 51 " ideal model delta sigma weight residual 121.54 127.71 -6.17 1.91e+00 2.74e-01 1.04e+01 angle pdb=" CA THR K 5 " pdb=" CB THR K 5 " pdb=" OG1 THR K 5 " ideal model delta sigma weight residual 109.60 105.02 4.58 1.50e+00 4.44e-01 9.33e+00 angle pdb=" CG MET A 669 " pdb=" SD MET A 669 " pdb=" CE MET A 669 " ideal model delta sigma weight residual 100.90 94.18 6.72 2.20e+00 2.07e-01 9.32e+00 angle pdb=" CA GLN K 6 " pdb=" C GLN K 6 " pdb=" O GLN K 6 " ideal model delta sigma weight residual 121.58 118.25 3.33 1.12e+00 7.97e-01 8.84e+00 ... (remaining 3625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 1407 15.67 - 31.33: 128 31.33 - 46.99: 38 46.99 - 62.66: 6 62.66 - 78.32: 3 Dihedral angle restraints: 1582 sinusoidal: 634 harmonic: 948 Sorted by residual: dihedral pdb=" CA MET A 669 " pdb=" C MET A 669 " pdb=" N LYS A 670 " pdb=" CA LYS A 670 " ideal model delta harmonic sigma weight residual 180.00 156.54 23.46 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA LEU A 657 " pdb=" C LEU A 657 " pdb=" N ASN A 658 " pdb=" CA ASN A 658 " ideal model delta harmonic sigma weight residual 180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CB MET H 34 " pdb=" CG MET H 34 " pdb=" SD MET H 34 " pdb=" CE MET H 34 " ideal model delta sinusoidal sigma weight residual 60.00 119.06 -59.06 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 256 0.044 - 0.089: 94 0.089 - 0.133: 27 0.133 - 0.177: 8 0.177 - 0.222: 3 Chirality restraints: 388 Sorted by residual: chirality pdb=" CA ILE H 53 " pdb=" N ILE H 53 " pdb=" C ILE H 53 " pdb=" CB ILE H 53 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ILE K 48 " pdb=" N ILE K 48 " pdb=" C ILE K 48 " pdb=" CB ILE K 48 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" CA ILE K 2 " pdb=" N ILE K 2 " pdb=" C ILE K 2 " pdb=" CB ILE K 2 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.59e-01 ... (remaining 385 not shown) Planarity restraints: 456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 67 " -0.001 2.00e-02 2.50e+03 1.97e-02 6.82e+00 pdb=" CG PHE H 67 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE H 67 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE H 67 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE H 67 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE H 67 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE H 67 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 96 " -0.010 2.00e-02 2.50e+03 1.08e-02 2.90e+00 pdb=" CG TRP K 96 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP K 96 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP K 96 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP K 96 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP K 96 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP K 96 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 96 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 96 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP K 96 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 96 " -0.027 5.00e-02 4.00e+02 4.16e-02 2.76e+00 pdb=" N PRO H 97 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO H 97 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 97 " -0.023 5.00e-02 4.00e+02 ... (remaining 453 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 671 2.80 - 3.32: 2173 3.32 - 3.85: 4469 3.85 - 4.37: 5120 4.37 - 4.90: 9233 Nonbonded interactions: 21666 Sorted by model distance: nonbonded pdb=" OE1 GLU H 33 " pdb=" OH TYR H 50 " model vdw 2.274 3.040 nonbonded pdb=" O TYR K 49 " pdb=" OH TYR K 91 " model vdw 2.304 3.040 nonbonded pdb=" O ASP K 82 " pdb=" OH TYR K 86 " model vdw 2.332 3.040 nonbonded pdb=" OH TYR H 99 " pdb=" OE2 GLU A 675 " model vdw 2.363 3.040 nonbonded pdb=" NH1 ARG K 54 " pdb=" O ILE K 58 " model vdw 2.380 3.120 ... (remaining 21661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.880 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 2690 Z= 0.313 Angle : 0.815 7.089 3634 Z= 0.480 Chirality : 0.054 0.222 388 Planarity : 0.006 0.042 456 Dihedral : 13.801 78.321 964 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.35 % Allowed : 1.41 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.45), residues: 316 helix: -1.44 (0.45), residues: 77 sheet: -1.17 (0.59), residues: 92 loop : -1.39 (0.49), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP K 96 HIS 0.004 0.001 HIS A 667 PHE 0.034 0.003 PHE H 67 TYR 0.010 0.002 TYR K 49 ARG 0.005 0.001 ARG K 61 Details of bonding type rmsd hydrogen bonds : bond 0.20482 ( 108) hydrogen bonds : angle 8.41595 ( 297) SS BOND : bond 0.00286 ( 2) SS BOND : angle 1.09634 ( 4) covalent geometry : bond 0.00573 ( 2688) covalent geometry : angle 0.81488 ( 3630) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.311 Fit side-chains REVERT: H 83 ARG cc_start: 0.7425 (mtt180) cc_final: 0.6945 (mtt-85) REVERT: K 100 GLN cc_start: 0.8370 (mp10) cc_final: 0.8087 (mp10) REVERT: A 680 LYS cc_start: 0.8178 (mtpt) cc_final: 0.7557 (mmmt) REVERT: A 706 LYS cc_start: 0.7845 (tppt) cc_final: 0.7386 (tmtt) outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.1754 time to fit residues: 9.1387 Evaluate side-chains 42 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.0470 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN K 6 GLN K 38 HIS A 600 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.154664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.132791 restraints weight = 2937.543| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.91 r_work: 0.3405 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2690 Z= 0.152 Angle : 0.511 4.622 3634 Z= 0.280 Chirality : 0.041 0.157 388 Planarity : 0.004 0.032 456 Dihedral : 4.209 19.309 351 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.06 % Allowed : 7.75 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.47), residues: 316 helix: 0.79 (0.50), residues: 77 sheet: -1.01 (0.54), residues: 104 loop : -0.73 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 79 HIS 0.002 0.001 HIS A 660 PHE 0.009 0.002 PHE K 83 TYR 0.009 0.001 TYR K 49 ARG 0.004 0.001 ARG H 71 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 108) hydrogen bonds : angle 5.09827 ( 297) SS BOND : bond 0.00360 ( 2) SS BOND : angle 1.22839 ( 4) covalent geometry : bond 0.00355 ( 2688) covalent geometry : angle 0.50973 ( 3630) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.294 Fit side-chains REVERT: H 83 ARG cc_start: 0.7659 (mtt180) cc_final: 0.7097 (mtt-85) REVERT: A 680 LYS cc_start: 0.8210 (mtpt) cc_final: 0.7563 (mmmt) REVERT: A 706 LYS cc_start: 0.7823 (tppt) cc_final: 0.7198 (tmtt) outliers start: 3 outliers final: 1 residues processed: 46 average time/residue: 0.2173 time to fit residues: 11.5224 Evaluate side-chains 45 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 102 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 HIS A 600 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.152325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.130368 restraints weight = 2925.238| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.94 r_work: 0.3321 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2690 Z= 0.147 Angle : 0.483 4.624 3634 Z= 0.263 Chirality : 0.040 0.157 388 Planarity : 0.003 0.031 456 Dihedral : 4.048 17.319 351 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.41 % Allowed : 10.56 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.49), residues: 316 helix: 1.58 (0.53), residues: 83 sheet: -0.66 (0.55), residues: 102 loop : -0.73 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 79 HIS 0.003 0.001 HIS A 660 PHE 0.009 0.002 PHE K 83 TYR 0.009 0.001 TYR K 49 ARG 0.002 0.000 ARG H 71 Details of bonding type rmsd hydrogen bonds : bond 0.02883 ( 108) hydrogen bonds : angle 4.60035 ( 297) SS BOND : bond 0.00288 ( 2) SS BOND : angle 1.03285 ( 4) covalent geometry : bond 0.00345 ( 2688) covalent geometry : angle 0.48233 ( 3630) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: H 83 ARG cc_start: 0.7558 (mtt180) cc_final: 0.7018 (mtt-85) REVERT: A 680 LYS cc_start: 0.8101 (mtpt) cc_final: 0.7503 (mmmt) REVERT: A 706 LYS cc_start: 0.7817 (tppt) cc_final: 0.7171 (tmtt) outliers start: 4 outliers final: 4 residues processed: 48 average time/residue: 0.2025 time to fit residues: 11.2270 Evaluate side-chains 49 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 52 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 0.0870 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.149256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.126971 restraints weight = 2964.308| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.96 r_work: 0.3236 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2690 Z= 0.177 Angle : 0.512 4.642 3634 Z= 0.275 Chirality : 0.042 0.164 388 Planarity : 0.003 0.029 456 Dihedral : 4.202 15.989 351 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.82 % Allowed : 11.62 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.50), residues: 316 helix: 1.91 (0.54), residues: 82 sheet: -0.65 (0.55), residues: 101 loop : -0.54 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 79 HIS 0.003 0.001 HIS A 660 PHE 0.011 0.002 PHE K 83 TYR 0.009 0.001 TYR K 49 ARG 0.002 0.000 ARG K 24 Details of bonding type rmsd hydrogen bonds : bond 0.02724 ( 108) hydrogen bonds : angle 4.43906 ( 297) SS BOND : bond 0.00376 ( 2) SS BOND : angle 1.18819 ( 4) covalent geometry : bond 0.00421 ( 2688) covalent geometry : angle 0.51077 ( 3630) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: H 83 ARG cc_start: 0.7624 (mtt180) cc_final: 0.7079 (mtt-85) REVERT: A 680 LYS cc_start: 0.8134 (mtpt) cc_final: 0.7563 (mmmt) REVERT: A 706 LYS cc_start: 0.7811 (tppt) cc_final: 0.7148 (tmtt) outliers start: 8 outliers final: 4 residues processed: 49 average time/residue: 0.1786 time to fit residues: 10.2603 Evaluate side-chains 48 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 52 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.153052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.131371 restraints weight = 2919.241| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.86 r_work: 0.3276 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2690 Z= 0.178 Angle : 0.500 4.648 3634 Z= 0.268 Chirality : 0.041 0.164 388 Planarity : 0.003 0.028 456 Dihedral : 4.175 16.089 351 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.93 % Allowed : 10.92 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.50), residues: 316 helix: 2.21 (0.54), residues: 82 sheet: -0.62 (0.55), residues: 99 loop : -0.48 (0.57), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 96 HIS 0.003 0.001 HIS A 660 PHE 0.011 0.002 PHE K 83 TYR 0.010 0.001 TYR K 49 ARG 0.002 0.000 ARG K 54 Details of bonding type rmsd hydrogen bonds : bond 0.02643 ( 108) hydrogen bonds : angle 4.39189 ( 297) SS BOND : bond 0.00383 ( 2) SS BOND : angle 1.13001 ( 4) covalent geometry : bond 0.00424 ( 2688) covalent geometry : angle 0.49906 ( 3630) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: H 31 ASP cc_start: 0.8295 (t0) cc_final: 0.7526 (t0) REVERT: H 83 ARG cc_start: 0.7648 (mtt180) cc_final: 0.7166 (mtt-85) REVERT: K 6 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7877 (mt0) REVERT: A 680 LYS cc_start: 0.8184 (mtpt) cc_final: 0.7659 (mmmt) REVERT: A 706 LYS cc_start: 0.7905 (tppt) cc_final: 0.7285 (tmtt) outliers start: 14 outliers final: 9 residues processed: 55 average time/residue: 0.1665 time to fit residues: 10.7594 Evaluate side-chains 56 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 19 optimal weight: 0.4980 chunk 6 optimal weight: 0.0070 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 0.0980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.153266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.130115 restraints weight = 2967.360| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.08 r_work: 0.3270 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2690 Z= 0.105 Angle : 0.434 4.648 3634 Z= 0.234 Chirality : 0.039 0.160 388 Planarity : 0.003 0.029 456 Dihedral : 3.821 15.290 351 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.82 % Allowed : 14.79 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.50), residues: 316 helix: 2.78 (0.54), residues: 82 sheet: -0.62 (0.53), residues: 102 loop : -0.56 (0.57), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 96 HIS 0.002 0.001 HIS A 660 PHE 0.008 0.001 PHE K 83 TYR 0.009 0.001 TYR K 91 ARG 0.001 0.000 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.02275 ( 108) hydrogen bonds : angle 4.01799 ( 297) SS BOND : bond 0.00191 ( 2) SS BOND : angle 0.57854 ( 4) covalent geometry : bond 0.00240 ( 2688) covalent geometry : angle 0.43379 ( 3630) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: H 31 ASP cc_start: 0.8178 (t0) cc_final: 0.7398 (t0) REVERT: H 83 ARG cc_start: 0.7522 (mtt180) cc_final: 0.7031 (mtt-85) REVERT: K 6 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7631 (mt0) REVERT: K 42 GLN cc_start: 0.8139 (mt0) cc_final: 0.7915 (mt0) REVERT: K 93 ASN cc_start: 0.7403 (p0) cc_final: 0.6478 (t0) REVERT: A 680 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7534 (mmmt) REVERT: A 706 LYS cc_start: 0.7793 (tppt) cc_final: 0.7155 (tmtt) outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 0.1971 time to fit residues: 11.1193 Evaluate side-chains 48 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain A residue 672 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.0270 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.155298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133323 restraints weight = 2997.634| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.88 r_work: 0.3284 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2690 Z= 0.178 Angle : 0.511 5.342 3634 Z= 0.271 Chirality : 0.041 0.164 388 Planarity : 0.003 0.027 456 Dihedral : 4.106 17.335 351 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.23 % Allowed : 13.03 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.50), residues: 316 helix: 2.64 (0.54), residues: 82 sheet: -0.66 (0.53), residues: 100 loop : -0.52 (0.57), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 79 HIS 0.003 0.001 HIS A 660 PHE 0.012 0.002 PHE K 83 TYR 0.011 0.001 TYR K 49 ARG 0.002 0.000 ARG K 39 Details of bonding type rmsd hydrogen bonds : bond 0.02584 ( 108) hydrogen bonds : angle 4.18467 ( 297) SS BOND : bond 0.00381 ( 2) SS BOND : angle 1.10347 ( 4) covalent geometry : bond 0.00423 ( 2688) covalent geometry : angle 0.50990 ( 3630) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: H 31 ASP cc_start: 0.8316 (t0) cc_final: 0.7570 (t0) REVERT: H 33 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6638 (mt-10) REVERT: H 83 ARG cc_start: 0.7638 (mtt180) cc_final: 0.7177 (mtt-85) REVERT: K 6 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7826 (mt0) REVERT: A 657 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7953 (mt) REVERT: A 674 LYS cc_start: 0.7878 (mttt) cc_final: 0.7226 (tttt) REVERT: A 680 LYS cc_start: 0.8182 (mtpt) cc_final: 0.7710 (mmmt) REVERT: A 706 LYS cc_start: 0.7965 (tppt) cc_final: 0.7333 (tmtt) outliers start: 12 outliers final: 8 residues processed: 52 average time/residue: 0.1849 time to fit residues: 11.2677 Evaluate side-chains 53 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 672 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 21 optimal weight: 0.1980 chunk 30 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.153386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.130525 restraints weight = 2936.846| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.05 r_work: 0.3327 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2690 Z= 0.121 Angle : 0.452 4.698 3634 Z= 0.244 Chirality : 0.039 0.161 388 Planarity : 0.003 0.027 456 Dihedral : 3.884 17.169 351 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.58 % Allowed : 12.68 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.50), residues: 316 helix: 2.91 (0.54), residues: 82 sheet: -0.55 (0.54), residues: 99 loop : -0.38 (0.57), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 79 HIS 0.002 0.001 HIS A 660 PHE 0.009 0.001 PHE K 83 TYR 0.008 0.001 TYR K 91 ARG 0.001 0.000 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.02303 ( 108) hydrogen bonds : angle 3.97858 ( 297) SS BOND : bond 0.00227 ( 2) SS BOND : angle 0.65386 ( 4) covalent geometry : bond 0.00283 ( 2688) covalent geometry : angle 0.45220 ( 3630) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: H 31 ASP cc_start: 0.8201 (t0) cc_final: 0.7437 (t0) REVERT: H 33 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6587 (mt-10) REVERT: H 83 ARG cc_start: 0.7541 (mtt180) cc_final: 0.7060 (mtt-85) REVERT: K 6 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7670 (mt0) REVERT: K 93 ASN cc_start: 0.7408 (p0) cc_final: 0.6526 (t0) REVERT: A 657 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7853 (mt) REVERT: A 674 LYS cc_start: 0.7807 (mttt) cc_final: 0.7033 (tttt) REVERT: A 680 LYS cc_start: 0.8080 (mtpt) cc_final: 0.7536 (mmmt) REVERT: A 706 LYS cc_start: 0.7824 (tppt) cc_final: 0.7148 (tmtt) outliers start: 13 outliers final: 10 residues processed: 53 average time/residue: 0.1721 time to fit residues: 10.6940 Evaluate side-chains 54 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 672 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.149762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.126690 restraints weight = 2995.442| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.06 r_work: 0.3281 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2690 Z= 0.189 Angle : 0.516 4.714 3634 Z= 0.276 Chirality : 0.042 0.163 388 Planarity : 0.003 0.026 456 Dihedral : 4.155 18.039 351 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.93 % Allowed : 12.68 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.50), residues: 316 helix: 2.76 (0.54), residues: 82 sheet: -0.64 (0.53), residues: 99 loop : -0.39 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 79 HIS 0.004 0.001 HIS A 660 PHE 0.012 0.002 PHE K 83 TYR 0.011 0.002 TYR K 49 ARG 0.002 0.000 ARG K 39 Details of bonding type rmsd hydrogen bonds : bond 0.02596 ( 108) hydrogen bonds : angle 4.17985 ( 297) SS BOND : bond 0.00370 ( 2) SS BOND : angle 1.10739 ( 4) covalent geometry : bond 0.00449 ( 2688) covalent geometry : angle 0.51469 ( 3630) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: H 31 ASP cc_start: 0.8273 (t0) cc_final: 0.7518 (t0) REVERT: H 33 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6643 (mt-10) REVERT: H 83 ARG cc_start: 0.7605 (mtt180) cc_final: 0.7120 (mtt-85) REVERT: K 6 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7797 (mt0) REVERT: K 93 ASN cc_start: 0.7496 (p0) cc_final: 0.6597 (t0) REVERT: A 657 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7999 (mt) REVERT: A 674 LYS cc_start: 0.7796 (mttt) cc_final: 0.7041 (tttt) REVERT: A 680 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7563 (mmmt) outliers start: 14 outliers final: 11 residues processed: 56 average time/residue: 0.1745 time to fit residues: 11.3837 Evaluate side-chains 58 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 672 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 23 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.0670 chunk 16 optimal weight: 0.0270 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 0.0870 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.154441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.131997 restraints weight = 2972.694| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.01 r_work: 0.3350 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2690 Z= 0.105 Angle : 0.453 4.698 3634 Z= 0.244 Chirality : 0.038 0.158 388 Planarity : 0.003 0.028 456 Dihedral : 3.804 16.698 351 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.87 % Allowed : 14.08 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.50), residues: 316 helix: 3.16 (0.54), residues: 82 sheet: -0.48 (0.54), residues: 99 loop : -0.32 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 79 HIS 0.002 0.001 HIS A 660 PHE 0.009 0.001 PHE K 83 TYR 0.009 0.001 TYR K 91 ARG 0.005 0.000 ARG K 54 Details of bonding type rmsd hydrogen bonds : bond 0.02189 ( 108) hydrogen bonds : angle 3.89189 ( 297) SS BOND : bond 0.00138 ( 2) SS BOND : angle 0.41713 ( 4) covalent geometry : bond 0.00245 ( 2688) covalent geometry : angle 0.45345 ( 3630) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: H 31 ASP cc_start: 0.8196 (t0) cc_final: 0.7440 (t0) REVERT: H 33 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6573 (mt-10) REVERT: H 83 ARG cc_start: 0.7507 (mtt180) cc_final: 0.7044 (mtt-85) REVERT: K 6 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7549 (mt0) REVERT: K 93 ASN cc_start: 0.7375 (p0) cc_final: 0.6555 (t0) REVERT: A 674 LYS cc_start: 0.7782 (mttt) cc_final: 0.7088 (tttt) REVERT: A 680 LYS cc_start: 0.8068 (mtpt) cc_final: 0.7531 (mmmt) REVERT: A 706 LYS cc_start: 0.7899 (tppt) cc_final: 0.7156 (tmtt) outliers start: 11 outliers final: 6 residues processed: 49 average time/residue: 0.1866 time to fit residues: 10.6952 Evaluate side-chains 48 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain A residue 672 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 12 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.151105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.128284 restraints weight = 2973.659| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.03 r_work: 0.3280 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2690 Z= 0.171 Angle : 0.508 4.716 3634 Z= 0.271 Chirality : 0.041 0.162 388 Planarity : 0.003 0.027 456 Dihedral : 4.030 17.378 351 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.17 % Allowed : 14.08 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.50), residues: 316 helix: 3.00 (0.54), residues: 82 sheet: -0.55 (0.53), residues: 99 loop : -0.33 (0.57), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 79 HIS 0.004 0.001 HIS A 660 PHE 0.013 0.002 PHE K 83 TYR 0.010 0.001 TYR K 49 ARG 0.006 0.000 ARG K 54 Details of bonding type rmsd hydrogen bonds : bond 0.02479 ( 108) hydrogen bonds : angle 4.02825 ( 297) SS BOND : bond 0.00315 ( 2) SS BOND : angle 0.95610 ( 4) covalent geometry : bond 0.00408 ( 2688) covalent geometry : angle 0.50690 ( 3630) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1751.37 seconds wall clock time: 31 minutes 39.12 seconds (1899.12 seconds total)